Does the Pseudo-fusion filter discard chimeric reads completely?

hyeshik / poreplex

A versatile sequenced read processor for nanopore direct RNA sequencing

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Does the Pseudo-fusion filter discard chimeric reads completely? #11

Open RaverJay opened 5 years ago

RaverJay commented 5 years ago

Hey,

see title.

Also, is it not feasible to split the read und process/keep both fused reads?

Cheers

hyeshik commented 5 years ago

Hi, You’re right. The filter does not try rescue the parts from the detected fusions. We are currently working on improving the specificity of the detector to enable the feature you mentioned, but I expect that it would not be done in a mean time.

RaverJay commented 5 years ago

Alright. I was thinking that an experimental rescue mode might still be useful. Straight up discarding them all bears the risk of losing long reads that are potentially vital for assembly.

Even without the improvements you mentioned - detection of the middle adapter already gives you the adapter position and even an inexact split could yield enough adapter signal to demultiplex. At the very least for the half without the internal adapter.

Anyway, thanks for your time and consideration!